countLoops: Count the number of loops in a pedigree tree.
In rmsharp/nprcmanager: Genetic Tools for Colony Management

Description Usage Arguments Details Value Examples

Part of Pedigree Sampling From PedigreeSampling.R 2016-01-28

1	countLoops(loops, ptree)

`loops`	a named list of logical values where each named element is named with an `id` from `ptree`. The value of the list element is set to `TRUE` if the `id` has a loop in the pedigree. Loops occur when an animal's sire and dam have a common ancestor.
`ptree`	a list of lists forming a pedigree tree as constructed by `createPedTree(ped)` where `ped` is a standard pedigree dataframe.

Contains functions to build pedigrees from sub-samples of genotyped individuals.

The goal of sampling is to reduce the number of inbreeding loops in the resulting pedigree, and thus, reduce the amount of time required to perform calculations with SIMWALK2 or similar programs.

Uses the loops data structure and the list of all ancestors for each individual to calculate the number of loops for each individual.

A list indexed with each ID in the pedigree tree (ptree) containing the number of loops for each individual.

library(nprcgenekeepr)
exampleTree <- createPedTree(nprcgenekeepr::examplePedigree)
exampleLoops <- findLoops(exampleTree)
## You can count how many animals are in loops with the following code.
length(exampleLoops[exampleLoops == TRUE])
## You can count how many loops you have with the following code.
nLoops <- countLoops(exampleLoops, exampleTree)
sum(unlist(nLoops[nLoops > 0]))
## You can list the first 10 sets of ids, sires and dams in loops with
## the following line of code:
examplePedigree[exampleLoops == TRUE, c("id", "sire", "dam")][1:10, ]